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Structure of aart, a designed six-finger zinc finger peptide, bound to DNA

Academic Article
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Overview

authors

  • Segal, D. J.
  • Crotty, J. W.
  • Bhakta, M. S.
  • Barbas III, Carlos
  • Horton, N. C.

publication date

  • October 2006

journal

  • Journal of Molecular Biology  Journal

abstract

  • Cys2-His2 zinc fingers are one of the most common types of DNA-binding domains. Modifications to zinc-finger binding specificity have recently enabled custom DNA-binding proteins to be designed to a wide array of target sequences. We present here a 1.96 A structure of Aart, a designed six-zinc finger protein, bound to a consensus DNA target site. This is the first structure of a designed protein with six fingers, and was intended to provide insights into the unusual affinity and specificity characteristics of this protein. Most protein-DNA contacts were found to be consistent with expectations, while others were unanticipated or insufficient to explain specificity. Several were unexpectedly mediated by glycerol, water molecules or amino acid-base stacking interactions. These results challenge some conventional concepts of recognition, particularly the finding that triplets containing 5'A, C, or T are typically not specified by direct interaction with the amino acid in position 6 of the recognition helix.

subject areas

  • Amino Acid Sequence
  • Base Sequence
  • Crystallography, X-Ray
  • DNA
  • Glycerol
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Nucleic Acid Conformation
  • Peptides
  • Protein Binding
  • Protein Conformation
  • Zinc Fingers
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Research

keywords

  • Aart
  • peptide
  • structure
  • zinc finger
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Identity

International Standard Serial Number (ISSN)

  • 0022-2836

Digital Object Identifier (DOI)

  • 10.1016/j.jmb.2006.08.016

PubMed ID

  • 16963084
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Additional Document Info

start page

  • 405

end page

  • 421

volume

  • 363

issue

  • 2

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